A detailed mapping of calretinin immunohistochemical localization was completed for rat hindbrain. Major calretinin-immunoreactive neurons were found in the lateral and medical geniculate nuclei, substantia nigra, ventral tegmental area, interpeduncular nucleus, periaqueductal gray, mesencephalic trigeminal nucleus, superior and inferior colliculi, pontine nuclei, parabrachial nucleus, dorsal and laterodorsal tegmental nuclei, cochlear nuclei, vestibular nuclei, medullary reticular nuclei, nucleus of the solitary tract, area postrema, substantia gelatinosa of the spinal trigeminal nucleus and cerebellum. An mRNA probe using human calretinin sequence was used for in situ hybridization histochemistry. Results indicated a distribution of calretinin mRNA which is complimentary to previous immunohistochemical results. Calretinin (100 nM) was shown to inhibit phosphorylation of a 39 kDa protein found in rat brain synaptic membranes. The phosphorylation of other proteins was either unaffected or enhanced by the added calretinin. Combinations of calretinin and effectors which stimulate either calcium/calmodulin protein kinase or protein kinase C resulted in additive effects on the phosphorylation of several proteins, excluding the 39 kDa phosphoprotein. These results demonstrate, for the first time, an effect of calretinin on the phosphorylation of synaptic membrane proteins.